Open Access Open Access  Restricted Access Subscription or Fee Access

Review Fluorescent Nucleosides Analogues

Nada Elsharif


The use of fluorescent nucleoside analogues becomes increasingly important because of their remarkable benefits in many fields such as biotechnology, biophysical chemistry, as well as in the field of DNA nanotechnology. In recent years, there have been many scientists who are interested in developing novel candidate in this grouping of fluorophores for benefits in various investigations. In this review article, design, classification, and synthesis of some tC family fluorescent base analogues were briefly summarized

Keywords: extended nucleobase analogues, fluorescent nucleobase, isomorphic base analogues, polycyclic hydrocarbons, pteridines, tricyclic cytosine
[1] Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent nucleoside analogs: probes for investigating nucleic acid structure and function. Israel J Chem. 2013; 53(6–7): 366–378p. Doi:10.1002/ijch.201300010
[2] Wilhelmsson LM. Fluorescent nucleic acid base analogues. Quart Rev Biophys. 2010; 43(02): 159–183p. Doi:10.1017/s0033583510000090
[3] Elsharif NA. Design and synthesis of novel fluorescent nucleoside analogues. Electronic Theses and Dissertations. 2012, 182p. Available from:
[4] Khakshoor O, Kool ET. Chemistry of nucleic acids: impacts in multiple fields. Chem Commun. 2011; 47(25): 7018–7024p.
[5] Srivatsan S, Greco N, Tor Y. A highly emissive fluorescent nucleoside that signals the activity of toxic ribosome-inactivating proteins. Angew Chem Int Ed. 2008; 47(35): 6661–6665p.
[6] Srivatsan SG, Weizman H, Tor Y. A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing. Org Biomol Chem. 2008; 6(8): 1334–1338p. Doi:10.1039/b801054d.
[7] Sinkeldam RW, Greco NJ, Tor Y. Fluorescent Analogs of Biomolecular Building Blocks: Design, Properties, and Applications. Chem Rev. 2010; 110(5): 2579–2619p. Doi: 10.1021/cr900301e.
[8] Patil S, Otter B, Klein R. Synthesis of some new thieno[3,4-d]pyrimidines and their C-nucleosides. Heterocycl Chem. 1993; 30(2): 509–515p.
[9] Srivatsan SG, Tor Y. Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. J Am Chem Soc. 2007a; 129(7): 2044–2053p.
[10] Hawkins, M. E. Fluorescent pteridine probes for nucleic acid analysis. In: L. Brand, M.L. Johnson, editors. Fluorescence Spectroscopy Methods in Enzymology. Burlington: Academic Press; 2008, Chapter 10, pp. 201–231. Doi:10.1016/s0076-6879(08)03410-1.
[11] Rodgers BJ, Elsharif NA, Vashisht N, Mingus MM, Mulvahill MA, Stengel G, Kuchta RD, Purse BW. Functionalized tricyclic cytosine analogues provide nucleoside fluorophores with improved photophysical properties and a range of solvent sensitivities. Chemistry. 2014; 20: 2010–2015p. Doi:10.1002/chem.201303410.
[12] Wilson JN, Kool ET. Fluorescent DNA base replacements: reporters and sensors for biological systems. Org Biomol Chem. 2006; 4(23): 4265–4274p. Doi: 10.1039/B612284C.
[13] Secrist JA III, Barrio JR, Leonard NJ, Weber G. Fluorescent modifications of adenosine containing coenzymes. Biological activities and spectroscopic properties. Biochemistry. 1972; 11(19): 3499–3506p.
[14] Börjesson K, Preus S, El-Sagheer AH, Brown T, Albinsson B, Wilhelmsson. Nucleic acid base analog fret-pair facilitating detailed structural measurements in nucleic acid containing systems. J Am Chem Soc. 2009; 131(12): 4288–4293p.
[15] Okamoto A, Saito Y, Saito I. Design of base-discriminating fluorescent nucleosides. J Photochem Photobiol C: Photochem Rev. 2005; 6(3): 108–122p.
[16] Okamoto A, Tainaka K, Saito I. Clear distinction of purine bases on the complementary strand by a fluorescence change of a novel fluorescent nucleoside. J Am Chem Soc. 2003; 125(17): 4972–4973p. Doi: 10.1021/ja034090u.
[17] Gardarsson H, Kale AS, Sigurdsson ST. Structure–function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy. ChemBioChem. 2011; 12(4): 567–575p.
[18] Kimoto M, Mitsui T, Harada Y, Sato A, Yokoyama S, Hirao I. Fluorescent probing for RNA molecules by an unnatural base-pair system. Nucl Acids Res. 2011; 35(16): 5360–5369p. Doi:10.1093/nar/gkm508.
[19] Dumas A, Luedtke NW. Cation-mediated energy transfer in G-quadruplexes revealed by an internal fluorescent probe. J Am Chem Soc. 2010; 132(51): 18004—18007p. Doi: 10.1021/ja1079578.
[20] Hirose W, Sato K, Matsuda A. Selective detection of 5-formyl-2′-deoxyuridine, an oxidative lesion of thymidine, in DNA by a fluorogenic reagent. Angew Chem Int Ed. 2010; 49(45): 8392–8394p.
[21] Preus S, Börjesson K, Kilså K, Albinsson B, Wilhelmsson LM. Characterization of nucleobase analogue FRET acceptor tCnitro. J Phys Chem B. 2010; 114(2): 1050–1056p. Doi: 10.1021/jp909471b
[22] Saito Y, Miyamoto S, Suzuki A, Matsumoto K, Ishihara T, Saito I. Fluorescent nucleosides with 'on-off' switching function, pH-responsive fluorescent uridine derivatives. Bioorg Med Chem Lett. 2012; 22(8): 2753–2756p.
[23] Suzuki A, Takahashi N, Okada Y, Saito I, Nemoto N, Saito Y. Naphthalene-based environmentally sensitive fluorescent 8-substituted 2'-deoxyadenosines: application to DNA detection. Bioorg Med Chem Lett. 2013; 23(3): 886–892p.
[24] Krim J, Grünewald C, Taourirte M, Engels JW. Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2′-deoxyuridines. Bioorg Med Chem. 2012; 20(1): 480–486p.
[25] Riedl J, Ménová P, Pohl R, Orság P, Fojta M, Hocek M. GFP-like fluorophores as DNA labels for studying DNA-protein interactions. J Org Chem. 2012; 77(18): 8287–8293p.
[26] Nakano S, Fujii M, Sugimoto N. Use of nucleic acid analogs for the study of nucleic acid interactions. J Nucl Acids. 2011: 1–11. Doi:10.4061/2011/967098.
[27] Bhat B, Leonard NJ. Dimensional analogue of a dA·dT base pair devoid of propeller twist. J Am Chem Soc. 1992; 114(19): 7407–7410p.
[28] Gao K, Orgel LE. Nucleic acid duplexes incorporating a dissociable covalent base pair. Proc Nat Acad Sci USA. (1999; 96(26): 14837–14842p.
[29] Atwell S, Meggers E, Spraggon G, Schultz PG. Structure of a copper-mediated base pair in DNA. J Am Chem Soc. 2001; 123(49): 12364–12367p.
[30] Yi Cho H, Woo SK, Hwang G. Synthesis and photophysical study of 2′-deoxyuridines labeled with fluorene derivatives. Molecules. 2012; 17(1420–3049): 12061–12071p. Doi:10.3390/molecules171012061.
[31] Kato T, Kashida H, Kishida H, Yada H, Okamoto H, Asanuma H. Development of a robust model system of FRET using base surrogates tethering fluorophores for strict control of their position and orientation within DNA duplex. J Am Chem Soc. 2013; 135(2): 741–750p. Doi:10.1021/ja309279w.
[32] Bood M, Sarangamath S, Wranne M, Grøtli1 M, Wilhelmsson LM. Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications. Beilstein J Org Chem. 2018; 14, 114–129. Doi:10.3762/bjoc.14.7
[33] Lou C, Dallmann A, Marafini P, Gao R, Brown T. Enhanced H-bonding and ??-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue. Chem Sci. (2014; 5(10): 3836–3844p.
[34] Roth B, Schloemer LA. 5-Arylthiopyrimidines. 111. Cyclization of 4-hydroxy derivatives to 10H-pyrimido[5,4-b][1,4]benzothiazines(1,3-diazaphenothiazines). J Org Chem. 1963; 28(66): 2659–2672p. Doi:10.1021/jo01045a042.
[35] Roth B, Hitchings G. Correction – 5-Arylthiopyrimidines. II. 2- and 4-Alkylamino and 4-amino derivatives. J Org Chem. 1961; 26(12): 5260–5260p. Doi:10.1021/jo01070a631.
[36] Schaller H, Weimann G, Lerch B, Khorana HG. Studies on polynucleotides. XXIV. The stepwise synthesis of specific deoxyribopolynucleotides (4). Protected derivatives of deoxyribonucleosides and new syntheses of deoxyribonucleoside-3″ phosphates. J Am Chem Soc. 1963; 85(23): 3821–3827p. Doi:10.1021/ja00906a021.
[37] Beaucage S, Caruthers M. Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 1963; 22(20): 1859–1862p. Doi:10.1016/s0040-4039(01)90461-7.
[38] Wranne MS, Füchtbauer AF, Dumat B, Bood M, El-Sagheer AH, Brown T, Wilhelmsson LM. Toward complete sequence flexibility of nucleic acid base analogue FRET. J Am Chem Soc. 2017; 139(27): 9271–9280p. Doi:10.1021/jacs.7b04517.
[39] Napoli LD, Messere A, Montesarchio D, Piccialli G, Santacroce C. Synthesis of 4-substituted pyrimidine 2′,3′-dideoxynucleosides. Nucleosides Nucleotides. 1991; 10(8): 1719–1728p.
[40] Lin KY, Jones RJ, Matteucci ML. Tricyclic 2'-deoxycytidine analogs: syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J Am Chem Soc. 1995; 117(13): 3873–3874p. Doi: 10.1021/ja00118a026.
[41] Lin K-Y, Matteucci MD. A cytosine analogue capable of clamp-like binding to a guanine in helical nucleic acids. J Am Chem Soc. 1998; 120(33): 8531–8532p. Doi: 10.1021/ja981286z

Full Text:



  • There are currently no refbacks.